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Scottx611x/is tool based cleanup #2222

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merged 19 commits into from
Oct 17, 2017
Merged

Scottx611x/is tool based cleanup #2222

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42c722c
Remove conditionals and related code that isn't necessary now that we…
scottx611x Oct 10, 2017
7abd945
Update Analysis config key names to be uniform, and update schema
scottx611x Oct 10, 2017
5600afb
Remove unnecessary tests
scottx611x Oct 10, 2017
019be46
Now that our schema is more basic we don't need the file resolver in …
scottx611x Oct 10, 2017
b6c3b24
Remove comment
scottx611x Oct 12, 2017
498dafc
No need for intermediate value
scottx611x Oct 16, 2017
3bb48f9
Exception handling
scottx611x Oct 16, 2017
302dc2c
Fit on one line
scottx611x Oct 16, 2017
e42bb0e
No need for extra parens
scottx611x Oct 16, 2017
c143e28
Add note about atomic transactions
scottx611x Oct 16, 2017
c4fa720
Remove anti-pattern
scottx611x Oct 16, 2017
c1c8060
Fix bracket styling
scottx611x Oct 16, 2017
a26147e
Move JSONSchema paths into `base.py`
scottx611x Oct 16, 2017
a0a205d
Remove returns in analysis_manager/tasks.py
scottx611x Oct 16, 2017
2f1419f
Utilize a single JSON_SCHEMA_FILE_RESOLVER setting for all defined sc…
scottx611x Oct 16, 2017
4c5949a
Merge `origin/develop` into `is_tool_based_cleanup`
scottx611x Oct 16, 2017
abd16e9
Revert moving JSONSchema paths into `base.py`
scottx611x Oct 16, 2017
f310f72
Revert 2f1419f
scottx611x Oct 16, 2017
a63fcec
Favor `import jsonschema`
scottx611x Oct 17, 2017
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3 changes: 0 additions & 3 deletions refinery/analysis_manager/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,9 +73,6 @@ def refinery_import_state(self):
return get_task_group_state(self.refinery_import_task_group_id)

def galaxy_file_import_state(self):
return get_task_group_state(self.galaxy_import_task_group_id)

def tool_based_galaxy_file_import_state(self):
if self.galaxy_import_state and self.galaxy_import_progress != 0:
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galaxy_import_state is a field of AnalysisStatus. Is it necessary to check whether it exists?

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Yes, you can still construct an AnalysisStatus like so w/o a galaxy_import_state: AnalysisStatus.objects.create(analysis=analysis)

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Right but the field would actually exists with a default value, no?

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The default value for a blank=True is u'' which is still falsey

For example, this test case passes:

def test_analysis_status_galaxy_import_state_is_falsey_by_default(self):
        analysis_status = AnalysisStatus.objects.create(analysis=self.analysis)
        self.assertFalse(analysis_status.galaxy_import_state)

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Yes but the field is there, so checking for its existence is not necessary.

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Its necessary as far as I can tell.

One would need to assert that there has been a galaxy_import_state set and that some galaxy_import_progress has happened before going ahead and handing a response over to the front end to display.
Otherwise theres nothing meaningful for the UI to display yet.

I could imagine a scenario occurring where the galaxy_import_state is still equal to u'' and even though the galaxy_import_state field is present, passing that information along to the frontend without checking it first would yield odd results.

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OK but you are already checking it by self.galaxy_import_progress != 0

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Just because there is positive galaxy_import_progress doesn't mean that a valid galaxy_import_state has been set as well?

Something like AnalyisStatus.objects.create(analysis=<analysis>, galaxy_import_progress=2) Would break the UI with your proposed change

galaxy_file_import_state = [{
'state': self.galaxy_import_state,
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46 changes: 28 additions & 18 deletions refinery/analysis_manager/schemas/AnalysisConfig.json
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@@ -1,24 +1,34 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"allOf": [{"$ref": "BaseAnalysisConfig.json#"}],
"oneOf":[
{
"required": ["nodeSetUuid"],
"properties": {
"nodeSetUuid": {"$ref": "BaseAnalysisConfig.json#patterns/uuid"}
}
"type": "object",
"required": [
"user_id",
"study_uuid",
"tool_uuid",
"workflow_uuid"

],
"patterns": {
"uuid": {
"type": "string",
"pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"
}
},
"properties": {
"name": {
"type": "string"
},
"study_uuid": {
"$ref": "#/patterns/uuid"
},
"tool_uuid": {
"$ref": "#/patterns/uuid"
},
{
"required": ["nodeRelationshipUuid"],
"properties": {
"nodeRelationshipUuid": {"$ref": "BaseAnalysisConfig.json#patterns/uuid"}
}
"user_id": {
"type": "number"
},
{
"required": ["toolUuid"],
"properties": {
"toolUuid": {"$ref": "BaseAnalysisConfig.json#patterns/uuid"}
}
"workflow_uuid": {
"$ref": "#/patterns/uuid"
}
]
}
}
29 changes: 0 additions & 29 deletions refinery/analysis_manager/schemas/BaseAnalysisConfig.json
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